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The comfortable victory from pole position at a Shanghai circuit that last hosted a Grand Prix in 2019 was Verstappen's fourth in five races in 2024 and came after he also won the season's first Saturday sprint.
Verstappen, who becomes only the second driver to win three consecutive Japanese Grands Prix alongside seven-time world champion Michael Schumacher, now has a 13-point lead in the drivers standings over Perez.
It was Verstappen's first DNF (did not finish) since retiring from Albert Park in the 2022 race and ended his run of race wins at nine.
Sergio Perez was runner-up under the Jeddah Corniche floodlights, last year's winner taking the chequered flag 13.643 seconds behind his triple world champion teammate who now has a 15-point lead in the standings.
The BBC said it had seen a report by FIA compliance officer Paolo Basarri to its ethics committee in which a whistleblower claimed the president had intervened to overturn a penalty given to Aston Martin's Fernando Alonso.
Verstappen senior also denied involvement in the anonymous email.
The Dutch driver took the chequered flag 22.4 seconds clear of his team mate Sergio Perez driving a similar RB20.
Red Bull has said the investigation report will remain confidential.
The action starts in Bahrain on Saturday.
The teams, along with Formula One Management and the governing FIA, agreed to reorder the sessions on sprint weekends so that Friday has one free practice followed by a sprint qualifying 'shootout'.